Cant make blastn work using biopython and NCBIWWW qblast, any thoughts?
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19 months ago
ejeide1 ▴ 10

Hello all,

I’m a beginner level python user experiencing a problem using biopython. I’m taking an online bioinformatics course and the example that we’re working through right now is to take a fasta file (called myseq.fa in the following example), open it then read. Then using the NCBIWWW module we need to do a BLAST nt search using the single fasta sequence in the myseq.fa file. However when I do this I get a series of lines in return, some with error messages. I’m including everything below. Does any of this make sense? Any thoughts on how I can fix this?

>>> from Bio.Blast import NCBIWWW
>>> fasta_string = open("myseq.fa").read()
>>> result_handle = NCBIWWW.qblast("blastn", "nt", fasta_string)

Traceback (most recent call last):
  File "/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/urllib/request.py", line 1319, in do_open
    h.request(req.get_method(), req.selector, req.data, headers,
  File "/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/http/client.py", line 1230, in request
    self._send_request(method, url, body, headers, encode_chunked)
  File "/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/http/client.py", line 1276, in _send_request
    self.endheaders(body, encode_chunked=encode_chunked)
  File "/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/http/client.py", line 1225, in endheaders
    self._send_output(message_body, encode_chunked=encode_chunked)
  File "/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/http/client.py", line 1004, in _send_output
    self.send(msg)
  File "/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/http/client.py", line 944, in send
    self.connect()
  File "/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/http/client.py", line 1399, in connect
    self.sock = self._context.wrap_socket(self.sock,
  File "/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/ssl.py", line 500, in wrap_socket
    return self.sslsocket_class._create(
  File "/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/ssl.py", line 1040, in _create
    self.do_handshake()
  File "/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/ssl.py", line 1309, in do_handshake
    self._sslobj.do_handshake()
ssl.SSLCertVerificationError: [SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: unable to get local issuer certificate (_ssl.c:1108)

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/Bio/Blast/NCBIWWW.py", line 171, in qblast
    handle = _urlopen(request)
  File "/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/urllib/request.py", line 222, in urlopen
    return opener.open(url, data, timeout)
  File "/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/urllib/request.py", line 525, in open
    response = self._open(req, data)
  File "/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/urllib/request.py", line 542, in _open
    result = self._call_chain(self.handle_open, protocol, protocol +
  File "/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/urllib/request.py", line 502, in _call_chain
    result = func(*args)
  File "/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/urllib/request.py", line 1362, in https_open
    return self.do_open(http.client.HTTPSConnection, req,
  File "/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/urllib/request.py", line 1322, in do_open
    raise URLError(err)
urllib.error.URLError: <urlopen error [SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: unable to get local issuer certificate (_ssl.c:1108)>
>>>
NCBIWWW biopython qblast error • 704 views
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Please use the formatting bar (especially the code option) to present your post better. You can use backticks for inline code (`text` becomes text), or select a chunk of text and use the highlighted button to format it as a code block. I've done it for you this time.
code_formatting

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